2-238141076-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_198582.4(KLHL30):c.322C>T(p.Arg108Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000205 in 1,609,156 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_198582.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152266Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000530 AC: 13AN: 245088Hom.: 0 AF XY: 0.0000299 AC XY: 4AN XY: 133712
GnomAD4 exome AF: 0.0000213 AC: 31AN: 1456890Hom.: 0 Cov.: 76 AF XY: 0.0000221 AC XY: 16AN XY: 724116
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152266Hom.: 0 Cov.: 34 AF XY: 0.0000269 AC XY: 2AN XY: 74390
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.322C>T (p.R108C) alteration is located in exon 2 (coding exon 1) of the KLHL30 gene. This alteration results from a C to T substitution at nucleotide position 322, causing the arginine (R) at amino acid position 108 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at